Identification of a clinically relevant pathogen requires great time, expense and expertise. Once clinical suspicion is raised that an infection is present, cultures are typically obtained from relevant sites from the patient and the patient is started on empiric antibiotic treatment. Isolation of the offending microorganism currently is a long and arduous process that involves painstaking attention to detail, and begins with culture on select agar for 24 to 48 hours. For some pathogens, an enrichment step is used prior to culture in order to increase the sensitivity of the culture. Once a pathogen is identified, to determine the susceptibility of the pathogen to antimicrobial agents, the isolate needs to be sub-cultured for an additional 24 to 48 hours in the presence of select antibiotics in order to further guide treatment. The entire process of identification of a clinically relevant pathogen and determination of its antibiotic susceptibility may take at least 3 to 5 days.
In order to reduce the amount of time required to identify a pathogen and determine its susceptibility to an antibiotic, additional techniques may be employed. These include the use of chromogenic broth/agar to reduce the time spent during the initial culture step, or the use of nucleic acid amplification technology (NAAT) to identify a specific pathogen after an enrichment step. If resistance determinants commonly found in a specific pathogen are known, these may be used to identify resistant pathogens by NAAT, further decreasing the time required to identify a specific microorganism. For example, in the determination of antenatal maternal colonization by group B streptococcus (GBS), both chromogenic agar/broth and nucleic acid amplification detection strategies have been employed. However, in situations in which a negative result is obtained by NAAT, the CDC recommends that culture still be performed. Furthermore, culture is required if antibiotic susceptibility is desired. All of these techniques involve additional resources and training, and are not always readily available.
In a recent policy paper released by the Infectious Diseases Society of America (IDSA), a call was made for the development of more rapid tests for the identification of clinically relevant pathogens, with the goal of providing better direction to the clinician in providing targeted treatment. This public policy statement cites a known deficiency in the common practice of empirically treating infections, with the concern that this practice allows for resistance against antibiotics to develop, ultimately rendering our tools useless in treating these infections. While penicillin-resistant GBS has not yet been associated with clinical disease, resistance against clindamycin is prevalent. Furthermore, resistance of Enterococcus against vancomycin has increased, and very recently, a strain of Neisseria gonorrhea was found to be resistant to cephalosporins. These three disparate organisms illustrate a range in the response to our directed approach in both prophylaxis and treatment. Indeed, they illustrate an evolution in microbial defensive mechanisms against our available antibiotics. Resistance of Enterococcus to vancomycin is well established, and continues to be a pressing concern. Many have warned of the impending development of cephalosporin resistance with gonorrhea, and this has been recently documented. Finally, the routine practice of intrapartum prophylaxis against GBS has raised concern not only that GBS will develop resistance, but other organisms will eventually be selected for, and many fear that this is already occurring with the increased incidence of neonatal sepsis due to E. coli. 
Early-onset neonatal sepsis has been shown to cause significant morbidity and mortality. Since the introduction of the CDC's guidelines for intrapartum chemoprophylaxis, the incidence of early-onset sepsis due specifically to GBS has decreased significantly. These guidelines recommend the antepartum screening of all pregnant patients between 35-37 weeks via a vaginal-rectal swab. For patients who are not able to be screened (preterm labor), the CDC recommends prophylaxis based on risk factors, including prematurity, history of an infant with GBS-sepsis, or prolonged rupture of membranes. While this approach has been widely accepted in the United States, there is concern that many patients are being exposed to antibiotics unnecessarily, and in doing so, antimicrobial resistance may develop.
Currently, isolation of GBS from a patient's vaginal-rectal specimen may occur one of two ways: culture, or by NAAT. Both methods have inherent strengths and weaknesses. Culture requires up to 48 hours, and samples may be overgrown by competing organisms. In addition, classic beta-hemolysis may be difficult to see in some clinical isolates, or completely absent. Moreover, when GBS is detected, additional steps are often required to ensure that false positives are ruled out. Recently, several products have become available which aid in the detection of GBS, with chromogenic broth/agar being the most notable.
NAAT offers great promise with the potential to streamline the process of pathogen detection. With this technique, a primer is generated which is targeted against DNA specific for GBS, and if GBS is present, even in very small amounts, it may be detected through amplification of the genetic material. Several commercial tests are available for detection of GBS, and one of these has been shown to allow for detection in less than 45 minutes. NAAT has deficiencies, however: the use of specialized equipment requires repeated measures for quality control and to prevent contamination; many laboratories will batch samples and run them at once, reducing the rapidity of the test; and NAAT does not allow for the detection of microbial strains which have developed de novo resistance. This is a significant shortcoming, since determination of de novo resistance of GBS against a specific antibiotic requires an additional culture period.
There exists an urgent need, therefore, for the development of a rapid assay with high specificity and sensitivity, which allows for simultaneous identification of a pathogen and for determination of the pathogen's antimicrobial susceptibility.